<html>
<title>Blast</title>
<body style="padding:20px;width:650px;font-family:Times">
<h2>Blast against the TCW database sequences</h2>
Enter a sequence, or sequences, into the entry box. 
Enter the E-value threshold, and choose the desired output format. 
Then press "Run Blast".
<p>
The results are shown in the bottom half of the panel. A "Save Results" button
is shown, which saves to a file. If tabular format is chosen, then you can
select a row and press "View Selected Sequence" to see the detail for
that database sequence. 
<p>
<i>Important:</i> if you enter multiple sequences, the fasta headers must be included!
<p>
<i>Important:</i> If your sequence contains characters other than A,G,C,T, or N, it will
be blasted as a protein sequence!



<h2>Blast software setup</h2>

If the blast programs are not found automatically then 
you will see an entry box to browse to the directory holding the blast
programs. Once you locate this directory, it will be used for the duration of the session.

<h3>Standalone use</h3>
It is recommended to install blast+, using the standard installation procedure, 
such that the programs are in your run path. If the programs aren't in your path,
you will need to set the "blast_path" parameter in HOSTS.cfg, 
e.g.
<p>
blast_path=/usr/local/ncbi/blast/bin
<p>
Note, enter the <t>directory</i> where the blast programs are located.

<h3>Web applet use - MacOSX</h3>

On OSX, if you have installed blast+ to the default install location /usr/local/ncbi/blast, 
then the TCW applet will find it. For different locations, you will need to enter the blast
directory manually (see above). 
<p>
Blast+ on MAC is really simple, just download from
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+.dmg
and click to open it, run setup, follow all defaults.

<h3>Web applet - other platforms</h3>

On other platforms, you will probably need to enter the blast directory manually (see above).   

<h3>Legacy blast</h3>

TCW also supports the legacy blast programs blastall, megablast; however, 
 blast+ will be used by default.